FDMNES

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An application for first-principles calculation based on density functional theory (DFT) optimized for X-ray spectroscopy analysis. Theoretical prediction and data fitting for X-ray spectroscopy such as XANES(X-ray absorption fine structure), XMCD(X-ray magnetic circular dichroism), RXD(resonant X-ray diffraction) can be preformes. This application employs a fully relativistic LSDA calculation based on the finite element method, and also supports the LDA+U method and the TD-DFT calculation.

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Avogadro

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

An open-source application of molecular modeling/editing for quantum chemical calculation. This application supports graphical user interface (GUI) for input-file preparation for software of quantum chemical calculation such as GAMESS, Gaussian, etc., and displays their results by reading output files. It can also make movies in the formats of vector graphics, POV-Ray, and so on.

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exciting

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

An open-source application for first-principles calculation based on all-electron calculations. In addition to ground-state energy and forces on atoms obtained by density functional theory, it focuses on investigation of excited state properties using time-dependent density functional theory as well as many-body perturbation theory. It is parallelized using MPI and is also optimized for multithreaded math libraries such as BLAS and LAPACK.

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MMSP

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

A collection of C++ interfaces for simulation of mesoscale properties based on grid data. By using provided header files, one can easily construct programs for simulation of various phenomena such as solidification, crystal growth, and spinodal decomposition, based on a Monte Carlo method, cellar automaton, and a phase-field method. This interface supports parallel computing by MPI, and also provides converters of output files for visualization software such as ParaView.

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VMD

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

An open-source application for modeling, visualization, and analysis of biomolecule systems such as proteins, nuclear acids, and lipid bilayers. This application visualizes biomolecules by reading Protein Data Bank (PDB) files. It supports various options in rendering and coloring of molecules, and also can animate the result of a molecular dynamics simulation.

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k-ep

  • Level of openness 3 ★★★
  • Document quality 1 ★☆☆

Fortran codes for computing the specified k-th eigenvalue and eigenvector for generalized symmetric definite eigenvalue problems. Sylvester’s law of inertia is employed as the fundamental principle in computations, and the sparse direct linear solver (MUMPS) is used in the main routine. By inputting Hamiltonian and its overlap matrices, user can compute electron’s energy and its wave function in the specified k-th energy level.

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NetKet

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

NetKet is an open-source project delivering cutting-edge methods for the study of many-body quantum systems with artificial neural networks and machine learning techniques. Users can perform machine learning algorithms to find the ground-state of many-body Hamiltonians such as supervised learning of a given state and optimization of neural network states by using the variational Monte Carlo method.

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Bilbao Crystallographic Server

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

Web server that offers various crystallographic tools free of charge. The server offers over 70 tools/utilities related to space group, magnetic space group, representation theory, scattering theory, etc. The tools are accessed through a web interface.

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cdview

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

An open-source application for visualization of many-particle systems. With simple operation by graphical user interface (GUI) or by command line, this application can visualize particle positions obtained from molecular dynamics simulation as well as three-dimensional scalar quantities such as potential energies. It supports various display options on kinds and shapes of particles, and can also visualize bond formation between particles.

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PyMOL

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An application for visualization of biopolymers. This application can visualize biopolymers by using its original command line and graphical user interface, more than 600 settings for visualization, and more than 20 visualization schemes. This application also supports more than 30 file formats such as PDB and multi-SDF, and can utilize sophisticated visualization methods such as the ray tracing.

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